E76K Mutation Promotes SHP2 Activation by Rewiring Allosteric Networks That Drives Conformational Transitions

The E76K mutation in protein tyrosine phosphatase (PTP) SHP2 is a recurrent driver of developmental disorders and cancers, yet the mechanism by which this single-site substitution promotes persistent activation remains elusive. Here, we combine path-based conformational sampling, unbiased molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) to elucidate how E76K reshapes the activation landscape and regulatory architecture of SHP2. Using a minimum-action trajectory derived from experimentally determined closed and open structures, we generated representative transition intermediates to guide the unbiased MD simulations. This strategy captured a thermodynamically relevant ensemble spanning the full activation process. MSMs analyses revealed that E76K flattens the energy landscape, stabilizes activation-prone conformations, and accelerates conformational transitions into catalytically competent states. NRI further uncovered a rewiring of allosteric communication networks, characterized by increased interdomain coupling and an elevated centrality of key relay residues. Shortest-path and temporal analyses revealed that the E76K-induced network remodeling precedes and facilitates domain opening, linking topological reorganization to structural activation. Together, our study provides a dynamic and mechanistic framework for understanding SHP2 activation by oncogenic mutation and illustrates the power of integrating ensemble modeling with interpretable network inference to dissect allosteric regulation.